Structure and Properties of Amino Acids

Structure and Properties of Amino Acids Nature s most versatile building blocks. 

Spider webs, animal hair and muscle, egg whites, and hemoglobin (the molecule that transports oxygen in the body to where it is needed) are all proteins. Peptides are oligomers of amino acids that play important roles in many biological processes. For example, the peptide hormone insulin controls our blood sugar levels, bradykinin controls our blood pressure, and oxytocin regulates uterine contraction and lactation. Thus, proteins, peptides, and amino acids are essential to the structure, function, and reproduction of living matter. In this chapter, we will first discuss the structure and properties of amino acids, then the properties of peptides, and finally the structures of proteins. 

In this chapter, we will explore the structure and properties of amino acids, and we will see how they function as the building blocks that nature employs to assemble Important biological compounds called peptides and proteins. These compounds serve a wide array of functions, as we will see later in this chapter. This chapter focuses on the structure, properties, function, and synthesis of amino... 

These are exciting times for peptide based materials. The number of investigators in this field and consequently the number of publications in this area have increased tremendously in recent years. Not since the middle of the past century has there been so much activity focused on the physical properties of peptidic materials. Then, efforts were focused on determination of the fundamental elements that make up protein structures, leading to the discoveries of the a—helix and the (3-sheet. Many years of study followed where the propensities of individual and combinations of amino acids to adopt and stabilize these structures were investigated. Now, this knowledge is being applied to the preparation, assembly, and use of peptide based materials with designed sequences. This volume summarizes recent developments in all these areas. 

Controllable Assembly, Structures, and Properties of Lanthanide-Transition Metal-Amino Acid Clusters... 

Abstract Amino acids are the basic building blocks in the chemistry of life. This chapter describes the controllable assembly, structures and properties of lathanide(III)-transition metal-amino acid clusters developed recently by our group. The effects on the assembly of several factors of influence, such as presence of a secondary ligand, lanthanides, crystallization conditions, the ratio of metal ions to amino acids, and transition metal ions have been expounded. The dynamic balance of metalloligands and the substitution of weak coordination bonds account for the occurrence of diverse structures in this series of compounds. 

Scientists carry out searches on databases. Each EST of interest can be compared with sequences in proteins, and the degree of match can be determined. A technique called threading is used. This involves using data on three-dimensional (3D) protein structure, coupled with knowledge of the physicochemical properties of amino acids, to determine if the amino acid sequence is likely to fold in the same way as a sequence for which the structure is known. In this way, more information about the putative target protein can be assessed. 

By using recombinant DNA techniques, modifications in the protein backbone, such as additions, deletions and alterations of amino acids, are easily achieved. These modifications can contribute to improved pharmacokinetic properties of the construct. Additions may consist of the introduction of residues that allow covalent conjugation of drug molecules. Deletions of amino acids can employed to remove membrane-bound regions of a protein, thereby increasing its solubility. Single amino acid modifications can be used to minimize antibody responses and alter the binding specificity and/or the three-dimensional structure of a certain protein. 

Protein structure and function are the topics of this and the next three chapters. We begin with a description of the fundamental chemical properties of amino acids, peptides, and proteins. 

In the first three chapters of part 2 we discuss the basic structural and chemical properties of proteins. In this chapter we concentrate on the structural and chemical properties of amino acids, peptides, and polypeptides—the building blocks of proteins. From our presentation you will learn the following ... 

Part 2, Protein Structure and Function, contains four chapters that relate to the structures and functions of proteins. In chapter 3, The Building Blocks of Proteins Amino Acids, Peptides, and Polypeptides, we discuss basic structural and chemical properties of amino acids, peptides and polypeptides. In chapter 4, The Three-Dimensional Structures of Proteins, we describe how and why polypeptide chains fold into long fibrous molecules in some cases, or into compact globular molecules in other cases. In chapter... 

Physicochemical properties of amino acids are very useful descriptors for understanding the structures and properties of proteins. These properties are expressed numerically in indexes that can be retrieved from the AAindex database. Design an index database of physicochemical properties of amino acids with Microsoft Access that may facilitate the data retrieval according to their chemical similarities ... 

There are several indications that a crystalline solid is the most appropriate state to model the protein interior (Chothia, 1984). The very fact that protein structures can be determined to high resolution by X-ray diffraction is indicative of the crystalline nature of the protein. Additionally, the packing density and volume properties of amino acid residues in proteins are characteristic of amino acid crystals (Richards, 1974, 1977). In spite of the apparent crystallinity of the protein interior, most model compound studies have investigated either the transfer of compounds from an organic liquid into water (see, for example, Nozaki and Tanford, 1971 Gill et al., 1976 Fauch-ere and Pliska, 1983), or the association of solute molecules in aqueous solution (see, for example, Schellman, 1955 Klotz and Franzen, 1962 Susi et al., 1964 Gill and Noll, 1972). Both these approaches tacitly assume a liquidlike protein interior. 

The properties of a protein depend primarily on its three-dimensional structure. The sequence of amino acids in the polypeptide chain is termed its primary structure. Its secondary structure is the shape of the backbone polypeptide chain. Remember that each amide group is planar, but the chain can have various conformations about the bond between the a-carbon and the nitrogen. The tertiary structure is the overall three-dimensional shape of the protein, including the conformations of the side chains. 

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